SNPs Screening And Genetic Diversity Analysis Of Loquat (Eriobotrya Japonica Lindl.)

Loquat(Eriobotrya japonica Lindl.) is a kind of subtropical evergreen fruit tree that blooms in fall and early winter. It belongs to the Maloideae subfamily of the Rosaceae beside apple and pear. The fruit is delicious and popular. The widely cultivated loquat has more than three seeds, while its flesh is very thin with low edible rate and the fruit is not easily to be processed. In our study, seedless triploid had been selected which is more edible and easily to be processed than the existing varieties from nature germplasm. In addition, it has very high production value. In recent years, the investigation of biological traits and genetic has been carried out in our institute. And a number of large-fruit and seedless strains that are preparing to be applied for the validation of new variety has been selected.In this study, we analyzed the single nucleotide polymorphism of part of triploid (’Dawuxing",’Longquan No.1’) and its diploid by comparing sequence differences. And we assess the diversity of Eriobotrya germplasm using the sites detected. SNP was analyzed from the transcriptome sequencing results of’Longquan No.1"diploid and triploid B355. The main results are as follows:1、We designed the primers according to the sequences registered in the NCBI website and EST sequences. We selected7primers producing single nucleotide polymorphism from20designed primers.2、We cloned and sequenced the seven genes and aligned all the fragments of the each gene.15SNPs were detected in CCoAoMT,84in DXS,38in HSP70,48in IDI,27in S6PDH,7in matK, and168in squalene epoxidase2. According to the types of substitution, the number of transition is241and the transversion is144. The transition is obviously more than the transversion, and the sites of SNP are not identical.3、The statistics that were generated by DnaSP software5.0show that the haplotype diversity of CCoAoMT, DXS, HSP70, IDI, S6PDH, matK and squalene epoxidase2are respectively0.486,0.973,0.918,0.548,0.767,0.324,0.947. The results showed that the genetic diversity of CCoAoMT, IDI and matK is general, but the genetic diversity of DXS、HSP70、S6PDH and squalene epoxidase2is high. The PIC of CCoAoMT, IDI, S6PDH, matK and squalene epoxidase2showed that there are great differences between different materials. The PIC of DXS and HSP70show that the the genes are not significantly different between different loquat.4、According to the result of SNP cluster,46materials were divided into three groups, most of ’Dawuxing’ and ’Longquan No.1’triploid are in the first group, the bootstrap test is100%, a small part of’Longquan No.1’triploid and their diploid are in the second and third group, the bootstrap test is92%and99%. B347is individually separate from others. A332and B335, B349and A376、 B329and A313、B414and A430are in together, and their node rate are respectively93%、88%、47%、97%. It means that the different varieties occurred at the same genetic variation in the same genetic background. A2and B352are in together, the node rate is93%. B2and B338are in together, the node rate is99%. It showed that we need to analysis SNP of multiple genes, in order to assess the genetic diversity in different No.s in different varieties. A348、B356、B350、B373. B378. B336、 B341、B242、B372、A379、B353、B357and B369are separated from other triploids, indicating that there are more abundant genetic diversity between different triploids and we can use the SNP markers for genetic diversity analysis.5、According to the transcriptome sequencing results of ’Longquan No.1’diploid and triploid B355, SNP was analyzed.115383SNP were detected in ’Longquan No.1’diploid, and121451SNP in B355.The number of transition is75966and the transversion is45485. Statistics show that the ratio of transition and transversion are37.55%and37.45%respectively, and the probability of their occurrence is2:1. The mutation between adenine and thymine is much more than those between cytosine and guanine, but the difference is not significant.